R: Using data table inside my own package: Error in lapply(.SD, mean) : object '.SD' not found

Question

Following up on this question , I built my own package, which makes use of data.table .

Inside the package, I use data.table to calculate means per column in a matrix according to another column.

Something in the lines of this:

datam <- cbind(matrix(rexp(100), 10), IN=c(rep(1,2), rep(2,3), rep(3,2), rep(4,1), rep(5,2)))
dd <- data.table::data.table(datam)
result <- dd[, lapply(.SD, mean), by=IN]

The only way I get it to work is including data.table in the Depends: field of my DESCRIPTION file AND import(data.table) in the NAMESPACE file.

Now I want to be able to call the function from my package that uses data.table like this:

mypackage::myfunction(...)

However, I get the following error:

Error in lapply(.SD, mean): object '.SD' not found

This error only goes away if I call my function after loading the package with library() , like this:

library(mypackage)
myfunction(...)

Since my package would be subsequently called from other packages, is there a way that I can make it work without having to use library() everytime, like I do for every other package I need a function from? Thanks

EDIT

I have just made a MWE package that reproduces the error. Please download from the Google Drive link below:

https://drive.google.com/open?id=1yHxmQeoIOx9VIuL4EBrFWlGDBstnKJQs

I used the usethis package to build it, in the usethis_myexample.R file.

The package itself is called myexample and is contained in the myexample-package folder. Inside there you can see the DESCRIPTION file contains data.table in the Imports section, and the NAMESPACE file contains import(data.table) .

There is only one function named aggregate_mean in the functions.R file inside the R folder.

Next to the myexample-package folder, there is a tests folder with a test file named mytest.R to run the aggregate_mean function like this:

mymat <- cbind(matrix(rexp(100), 10), IN=c(rep(1,2), rep(2,3), rep(3,2), rep(4,1), rep(5,2)))
mymat
mynewmat <- myexample::aggregate_mean(mymat, "IN")
mynewmat

I always encounter the error:

Error in lapply(.SD, mean): object '.SD' not found

Thanks!

Answer 1

As there is an reproducible exaple now in your question, I was able to dig into it.

I downloaded zip file from your link, unzip it, renamed myexample-package to mypackage . Then...

R CMD build myexample
R CMD INSTALL myexample_0.0.0.9000.tar.gz
R -q

then in R.

mymat <- cbind(matrix(rexp(100), 10), IN=c(rep(1,2), rep(2,3), rep(3,2), rep(4,1), rep(5,2)))
mymat                                                                  
# [1,] 0.83010264 0.4778802 1.15826121 0.304299143 0.5781483 1.81660550
# [2,] 0.03895798 2.3709480 0.69694839 0.730800823 0.3319984 0.53348461
# [3,] 0.03383199 0.2842029 1.74151827 1.019573035 0.1863635 0.89487309
# [4,] 0.53533254 0.2814782 0.78563371 0.309180422 1.4393098 1.07450638
# [5,] 0.53010142 1.3132409 0.67072292 1.212244007 0.1984360 0.06208641
# [6,] 0.45916016 0.5576434 0.67770401 0.056270575 0.5065829 0.83416626
# [7,] 0.25404953 0.2730706 0.01070633 0.132406274 1.6186573 0.37083771
# [8,] 3.42254715 0.6489950 0.81291881 0.003048744 1.3522848 0.18066361
# [9,] 1.29994319 0.3170614 1.71145805 1.141222719 1.1832478 0.18091907
#[10,] 0.23622615 0.4473482 3.07774816 1.441207092 0.9761152 0.28132707
#                                                IN
# [1,] 6.1868517 2.44880203 0.55261438 0.3459453  1
# [2,] 0.8177218 0.90554629 1.00106158 1.0427756  1
# [3,] 4.3910329 0.56068780 0.24262243 1.7036666  2
# [4,] 0.8712083 0.02439399 0.80927766 1.6596570  2
# [5,] 0.6613734 0.12954737 1.01661648 1.2446795  2
# [6,] 0.2858442 2.32610958 0.26553789 0.4856818  3
# [7,] 3.6628536 0.26447698 0.70633274 2.0283399  3
# [8,] 0.0515666 0.99916985 0.06102821 0.9413485  4
# [9,] 4.7781407 1.47764414 1.92598562 0.4581395  5
#[10,] 0.8770661 2.78552022 0.07543095 0.6886183  5
mynewmat <- myexample::aggregate_mean(mymat, "IN")
mynewmat
#   get        V1        V2        V3          V4        V5        V6        V7
#1:   1 0.4345303 1.4244141 0.9276048 0.517549983 0.4550734 1.1750451 3.5022868
#2:   2 0.3664220 0.6263073 1.0659583 0.846999155 0.6080364 0.6771553 1.9745382
#3:   3 0.3566048 0.4153570 0.3442052 0.094338425 1.0626201 0.6025020 1.9743489
#4:   4 3.4225471 0.6489950 0.8129188 0.003048744 1.3522848 0.1806636 0.0515666
#5:   5 0.7680847 0.3822048 2.3946031 1.291214905 1.0796815 0.2311231 2.8276034
#          V8         V9       V10 IN
#1: 1.6771742 0.77683798 0.6943604  1
#2: 0.2382097 0.68950553 1.5360010  2
#3: 1.2952933 0.48593531 1.2570109  3
#4: 0.9991699 0.06102821 0.9413485  4
#5: 2.1315822 1.00070829 0.5733789  5

So I am not able to reproduce your problem. I encourage you to follow the same steps as described above, to narrow down, if the issue lies somewhere in the way how you install your package. If you have more followup question, rather than editing question, best to put them in comments under my answer.

Hope that helps!

Answer 2

Add Imports: data.table to your package description and declare .datatable.aware <- TRUE somewhere in an R-File of your package.

That solved the problem for me.